Hi, That user's input can't use OpenMP, like the message says. So try the other options. (And again, don't run mpirun on a thread-MPI mdrun!)
Mark On Mon, Oct 10, 2016 at 1:02 PM Mahmood Naderan <mahmood...@gmail.com> wrote: > Sorry for the previous incomplete email. > > Program mdrun, VERSION 5.1 > Source code file: > /share/apps/chemistry/gromacs-5.1/src/programs/mdrun/resource-division.cpp, > line: 746 > > Fatal error: > OpenMP threads have been requested with cut-off scheme Group, but these are > only supported with cut-off scheme Verlet > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > > I read that document from that web site but didn't understand what is the > issue! > Thanks > > Regards, > Mahmood > > > > On Mon, Oct 10, 2016 at 2:29 PM, Mahmood Naderan <mahmood...@gmail.com> > wrote: > > > >mpirun -np 1 mdrun_mpi -v -ntomp 2 > > > > Agree with that. > > > > >This is not a problem to solve by running applications differently. You > > >will have users running jobs with single ranks/processes that use > > threading > > >of various kinds to fill the cores. That's a feature, not a bug. Either > > >configure PBS to cope with decades-old technology, or don't worry about > > it. > > > > I found this document > > ( > > https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/ > > Advanced_node_selection#Multithreading_using_OpenMP) > > That is what I want to be sure that number of threads and cores used for > > gromacs fits to the PBS stats. > > > > Instead of the variable, I wrote > > > > > > > > #PBS -l nodes=1:ppn=2 > > export OMP_NUM_THREADS=2 > > mpirun mdrun -v > > > > So that will use two cores with 4 threads totally and PBS should report 4 > > processors are occupied. > > However, gromacs failed with the following error > > > > > > > > > > Regards, > > Mahmood > > > > > > > > On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> Hi, > >> > >> Yeah, but that run is very likely > >> > >> a) useless because you're just running two copies of the same simulation > >> because you're not running MPI-enabled mdrun > >> b) and even if not, less efficient than the thread-MPI version > >> > >> mdrun -v -nt 2 > >> > >> c) and even if not, likely slightly less efficient than the real-MPI > >> version > >> > >> mpirun -np 1 mdrun_mpi -v -ntomp 2 > >> > >> top isn't necessarily reporting anything relevant. A CPU can be > nominally > >> idle while waiting for communication, but what does top think about > that? > >> > >> Mark > >> > >> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan <mahmood...@gmail.com> > >> wrote: > >> > >> > OK. I understood the documents. > >> > Thing that I want is to see two processes (for example) each consumes > >> 100% > >> > cpu. The command for that is > >> > > >> > mpirun -np 2 mdrun -v -nt 1 > >> > > >> > Thanks Mark. > >> > > >> > Regards, > >> > Mahmood > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/Support > >> /Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.